Greenawalt: #ampeurope2018 Shows results presented at #AACR18 (online https://t.co/roRLSiUyaj )
8:49am April 30th 2018 via Twitter Web Client
Greenawalt: #ampeurope2018 40 pts, WES, RNA-seq; muts called in paired T/N samples. Response was similar.
8:48am April 30th 2018 via Twitter Web Client
Greenawalt: #ampeurope2018 JAS1/2 LoF in preRx samples from CheckMate-142. PhII, non-randomized, mCRC or recurrCRC. dMMR/MSI-H >1 prior R
8:46am April 30th 2018 via Twitter Web Client
Danielle Greenawalt (BMS, USA) #ampeurope2018 Exploratory Analysis of (JAK1) Loss-of-Function (LoF) Mutations in Pa… https://t.co/03lqyQXRha
8:45am April 30th 2018 via Twitter Web Client
Roberts: #ampeurope2018 Increased LAG-3 mRNA exp post-Rx. Co-localization of LAG-3 w/MHC II may serve as checkpoint activation mechanism
8:42am April 30th 2018 via Twitter Web Client
Roberts: #ampeurope2018 '16 PNAS https://t.co/TaBWliRzwm
Roberts: #ampeurope2018 IgG4 Reltinimab is against LAG-3. Expression: correlated w/immune, inflamm markers by TCGA
8:41am April 30th 2018 via Twitter Web Client
Mustimbo Roberts (BMS) #ampeurope2018 Multitumor Profiling of Lymphocyte Activation Gene 3 (LAG-3) and Association… https://t.co/fJLx73FgzW
8:36am April 30th 2018 via Twitter Web Client
Q: Why only missense for ML? Roepman: #ampeurope2018 Fixed for the trial, now want to include indels, fusions too.
8:34am April 30th 2018 via Twitter Web Client
Q: How did they validate tumor content? Roepman: #ampeurope2018 GIAB cell line mixed, but still more work to do on their method.
8:33am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Can weed out structural variants in BRCA1; a clear benefit to their approach.
8:32am April 30th 2018 via Twitter Web Client
Q: WGS vs targeted? Roepman: #ampeurope2018 WGS is $, built a fresh-frozen workflow across all participants. SVs, b… https://t.co/OgqQOU3Tgo
8:31am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 No more Rx option, >200pt receive 'off-label' to-date in DRUP. Large coverage, Barcode for Life, SUTC credits
8:30am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Info about DRUP >500 pts enrolled (NB https://t.co/dvCbprZ5vi ) 30-35% benefit
8:29am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 DRUP - off-label study, showed ex of prostate ca after 7 lines of Rx! WGS shows high ML -> I-O in DRUP
8:28am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 They call TMB Mutational Load: used for eligability in 'DRUP' study ML >140
8:27am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Then derive a Tuor-Adjusted Variant Freq (TAF). Have also derived MSI and TMB almost 100% concord shown
8:25am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Adv correction for tumor purity: genome-wide Bi-Allelic Freq (BAF) observied w/CNV can get… https://t.co/RfZgKru48S
Roepman: #ampeurope2018 Report CNV, copy-gain and loss, SVs (NB: Hartwig dataset here: https://t.co/UVZbT46Pbh apply for access)
8:23am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Has ~2,800 metastatic pt data, pan-cancer, uniform processing from biopsy to database
8:21am April 30th 2018 via Twitter Web Client
Roepman: #ampeurope2018 Hartwig Medical Found. - WGS-based pt report, database for learning healthcare system.
Paul Roepman (Amsterdam, The Netherlands) #ampeurope2018 Comp. Molecular Char of Metastatic Cancer Using WGS – a Dutch National Initiative
8:20am April 30th 2018 via Twitter Web Client
Q: Newer content helpful? de Voer: #ampeurope2018 Only V5 mapping to compare, haven't looked at it.
7:03am April 30th 2018 via Twitter Web Client
Q: NTHL1 recessive, what about carriers? de Voer: #ampeurope2018 Tumors are analyzed from biallelic, now looking. But low #'s, further study
7:01am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Want more accurate var detection from FFPE; would like strand-spec capture of FFPE to remove artifacts
6:59am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Concludes: FFPE WES feasible; helps in their NTHL1 work on signatures, mutation evolution.
6:58am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Onto NTHL1 deficiency, and mutational processes in extracolonic tumors. Going after mutational signatures
6:57am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Shows surprising lack of concordance between XT HS and V5 SureSelect; but high stringency helps explain (!)
6:54am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Var absent from in-house DB, or <0.01% in ExAC or gnomAD; <20% or >80% VAF excluded. QC>200
6:52am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Somatic var detection in FFPE exomes: mapping to hg19 w/BWA, using unified genotyper; cp ge… https://t.co/HzD9E8LdYD
de Voer: #ampeurope2018 Now doing WES at 80x coverage; compares regular FFPE to HS XS FFPE to germline.
6:51am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 UMI-labeled input - median 244bp; library median insert about 290bp. First 16 sample results reported
6:48am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Extended to do SureSelect WES on FFPE. Before lib prep, add UMIs and PCR amplify. DIN scored, 10-200ng input
6:46am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 They study familiar, rare cancers and predisp. NTHL1 suspected. '16 ref https://t.co/S6v5mIPzg6
6:44am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Shows fig from '15 ref https://t.co/3feWMDeVt9 on types of FFPE damage
6:42am April 30th 2018 via Twitter Web Client
de Voer: #ampeurope2018 Usually FFPE insuff; bigger challenge is fixation process damaging DNA. Deamination and crosslinking.
6:41am April 30th 2018 via Twitter Web Client
#ampeurope2018 Richarda de Voer (Radboud Univ Netherlands) Challenges with using FFPE samples for NGS
6:40am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 Reviews DAKO offering for IHC, and NGS from QC, library prep and automation.
6:36am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 Shows interesting FFPE vs HMW coverage between good and poor quality FFPE samples; amplifiability x amplicon size
6:35am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 FFPE considerations: need assay designed for it; 0.6 mm3, or 4-8 slices; >20 tumor cellularity; UNG removing deaminatio
6:32am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 Smaller panels have lower cost, fewer incidental findings, easier to implement.
6:31am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 AIO 'all in one' SureSelect-based. SNPs, indels, CNV and fusion from 1 sample. Using XTHS sample prep tech, UMI compat
6:27am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 Preferred markers KRAS, MET, BRAF not testd. Using MASTR Plus (Multiplicom). MASTR reporter software has a QC component
Bossuyt: #ampeu18 For NSCLC: EGFR testing, perhaps ALK/ROS fusion test w/FISH. Minimally-req'd markers: EGFR, ALK and ROS fusion, amplf.
6:25am April 30th 2018 via Twitter Web Client
Bossuyt: #ampeu18 10d TAT: fix tissue, embed, H&E then IHC. NSCLC and SCLC for disease classification days 3-4. Day… https://t.co/E24KWA
6:24am April 30th 2018 via Twitter Web Client
Wouter Bossuyt (Agilent Product Manager, workshop) #ampeu18 Integrating NGS in a pathology workflow
6:22am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 June EFLM Conf in Mannhim DE The end of laboratory medicine as we know it? Handling disruption o… https://t.co/ovmaZJAYrf
6:15am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Limitation of ctDNA meas - method-spec error rate for MALDI high 50%; pyro 16%, real-time PCR 16… https://t.co/mQ4WKsYiVr
6:05am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Shows heat-induced frag, duplex PCR w/a spec pyroseq G/A ratio (G larger, A smaller PCR prod) https://t.co/CaofWJcbUW
6:01am April 30th 2018 via Twitter Web Client
Neumaier: #ampeu18 Just measuring 260/280 w/same DNAs, and quant numbers: all over the place. Pyro seq: sensitive to amt, quality
5:59am April 30th 2018 via Twitter Web Client
